The objective of this work is to advance the state-of-the-art in whole protein mixture analysis with heavy emphasis on electrodynamic ion traps as reaction vessels for unimolecular and ion/ion reaction chemistries. Whole protein tandem mass spectrometry has been largely restricted to only a few types of mass spectrometry technologies and has, for the most part, been based on electrospray ionization. This proposal will emphasize the use of linear ion traps, which can serve as stand-alone mass analyzers or can readily be interfaced with other forms of mass analysis. Furthermore, one aspect of the proposal is devoted to the gasphase conversion of singly charged ions to multiply charged ions, which will facilitate whole protein tandem mass spectrometry using desorption ionization methods, which tend to form singly charged ions. Such a development would enable technologies that are well-suited to the spatial interrogation of surfaces to enjoy the structural tools now largely restricted to multiply charged ions derived via electrospray ionization. Other aspects of the proposal promise to expand the use of ion/ion reactions for mixture analysis and for the derivation of structrual information from whole protein ions, including post-translationally modified species. Furthermore, this work promises to make much more widely accessible means for studying whole proteins and protein complexes without prior recourse to enzymatic digestion. Particular emphasis will be placed on improved understanding and performance of electrospray ionization and matrix assisted laser desorption ionization applied to protein mixtures, charge state manipulation reactions, including charge inversion and, in some cases, sequential charge inversion steps, ion/ion reactions that provide structural information that is complementary to collisional activation of protonated species, and instrumentation development focused on stand-alone linear ion trap instrumentation and linear ion traps coupled with orthogonal acceleration time-of-flight mass analysis.